Division of STD Prevention | Surveillance and Data Science Branch | Case-Based Surveillance Team | Last Modified: 12/19/22 

DEDUPLICATION STANDARDS FOR CHLAMYDIA AND GONORRHEA CASE 

REPORTS BASED ON LABORATORY TEST RESULTS 

JANUARY 2023 

BACKGROUND

National deduplication standards on the minimum amount of time between positive laboratory test 

results to trigger a report of a new case are included in the 2022 Chlamydia trachomatis and 2023 

Neisseria gonorrhoeae infection surveillance case definitions (1, 2). The deduplication standards were

informed by scientific literature on nucleic acid amplification tests (NAATs) that are commonly used to 

diagnose both infections, current Centers for Disease Control and Prevention (CDC) test of cure 

recommendations, a 2015 CDC assessment of STD surveillance practices in local and state jurisdictions, 

and feedback from STD surveillance programs during the process of updating the Council of State and 

Territorial Epidemiologists (CSTE) chlamydia and gonorrhea position statements. 

Chlamydia and gonorrhea can be diagnosed with a highly sensitive NAAT (3). A positive NAAT test 

result in the weeks following successful treatment may indicate residual genetic material rather than a 

new or persistent infection and should not be reported as a second case (4). Residual nucleic acid from 

bacteria rendered noninfective by antibiotics might still give a positive C. trachomatis NAAT result up 

to 4 weeks after therapy (3, 5). Detection of N. gonorrhoeae nucleic acid has been observed for up to 2 

weeks following therapy although the majority of patients who were treated effectively for gonorrhea 

had a negative NAAT 1 week after treatment (6). For these reasons, current CDC guidelines for 

chlamydia recommend test of cure to detect therapeutic failure for pregnant persons at 4 weeks. For 

any person diagnosed with pharyngeal gonorrhea, test of cure is recommended 7–14 days after initial 

treatment by using either culture or NAAT (3). 

A 2015 assessment of STD surveillance practices among CDC-funded project areas showed that the 

reported timeframe used for deduplicating chlamydia and gonorrhea case reports based on laboratory 

test results varied by jurisdiction and by pathogen. Sites reported using a range of 7 to 90 days for 

deduplication for both chlamydia and gonorrhea case report data. Most jurisdictions deduplicated case 

data when laboratory test results were within 30 days of each other: 57% of jurisdictions reported 30 

days for chlamydia and 54% of jurisdictions reported 30 days for gonorrhea. A few jurisdictions had 

additional deduplication rules for certain populations (e.g., different time periods for pregnant 

women). Several jurisdictions reported different time periods of deduplication for gonorrhea and 

chlamydia with some of these jurisdictions using a shorter time period to deduplicate gonorrhea cases. 

In jurisdictions that provided enough details, deduplication methods also varied across jurisdictions 

with 28% using automated deduplication within their surveillance information system, 20% using 

manual methods (e.g., data clerk deciding whether to enter the laboratory test result as a new case), 

and 22% using a combination of methods.

Feedback on deduplication standards was also collected from state and local STD surveillance 

programs during the process of updating the CSTE chlamydia and gonorrhea position statements. 
Division of STD Prevention | Surveillance and Data Science Branch | Case-Based Surveillance Team | Last Modified: 12/19/22 

During this process, jurisdictions were asked to review proposed deduplication standards for chlamydia 

and gonorrhea. While jurisdictions acknowledged that time to NAAT clearance varied by pathogen, 

several jurisdictions noted that it may be difficult to implement different deduplication time periods 

for each condition. Ultimately, the approved position statements updated the case definitions for 

chlamydia and gonorrhea to include national deduplication standards for case reports based on 

laboratory test results (1, 2). Although the specific wording used to describe the criteria to distinguish a 

new case is not identical in the two position statements, the deduplication standards are intended to 

be the same for both conditions. 

ACTION ITEMS

To strengthen national chlamydia and gonorrhea surveillance, CDC recommends that jurisdictions:

1. Learn about the national standards for deduplicating chlamydia and gonorrhea case reports

based on laboratory test results that are described in the current CSTE position statements for 

each condition (1, 2) and shown in Figure 1: deduplicate case reports if there is a previously 

reported case with a specimen collection date or documented treatment date in the prior 30 

days, AND no evidence of reinfection. 

2. Routinely review available laboratory, treatment completion, and partner services data to 

determine if a positive laboratory test result represents a prior, previously reported case that 

should not be reported as a new case. 

3. Apply the national deduplication standards within STD surveillance programs, incorporating a 

deduplication algorithm (Figure 1) into electronic surveillance information systems, if possible. 

4. Ensure that chlamydia and gonorrhea case report data are reviewed and deduplicated as 

appropriate prior to data submission to CDC.

ADDITIONAL CONSIDERATIONS

Jurisdictions should keep the following considerations in mind:

1. Deduplication standards are intended to inform reporting of chlamydia and gonorrhea cases for 

the purpose of disease surveillance. These standards are not intended to be used for clinical 

treatment purposes.

2. If a positive laboratory test result is not reported as a new case, it should be retained in the 

surveillance database to aid in patient follow-up and for ongoing chlamydia and gonorrhea 

surveillance activities.

RESOURCES

Figure 1 is a visual aid to help jurisdictions implement the algorithm for deduplicating chlamydia and 

gonorrhea case reports based on laboratory test results. 
Division of STD Prevention | Surveillance and Data Science Branch | Case-Based Surveillance Team | Last Modified: 12/19/22 

Figure 1. Algorithm for deduplicating chlamydia and gonorrhea case reports based on laboratory test 

results 

REFERENCES

1. Council of State and Territorial Epidemiologists (CSTE). Public Health Reporting and National Notification for

Infection Caused by Chlamydia trachomatis. 21-ID-06. Atlanta: CSTE; 2021. Available from: http://www.cste.org. 

2. Council of State and Territorial Epidemiologists (CSTE). Update to Public Health Reporting and National Notification 

for Infection Caused by Neisseria gonorrhoeae. 22-ID-03. Atlanta: CSTE; 2022. Available from: http://www.cste.org. 

3. Workowski KA, Bachmann LH, Chan PA, et al. Sexually Transmitted Infections Treatment Guidelines, 2021. MMWR 

Recomm Rep 2021;70 (No. RR 4): 1-187. 

4. Papp JR, Schachter J, Gaydos CA, Van der Pol B. Recommendations for the Laboratory-Based Detection of 

Chlamydia trachomatis and Neisseria gonorrhoeae – 2014. MMWR 2014;63(No. RR-2):1-19. 

5. Lazenby GB, Korte JE, Tillman S, Brown FK, Soper DE. A recommendation for timing of repeat Chlamydia 

trachomatis test following infection and treatment in pregnant and nonpregnant women. Int J STD AIDS 2017;28:

902–9. 

6. Bachmann LH, Desmond RA, Stephens J, Hughes A, Hook EW III. Duration of persistence of gonococcal DNA 

detected by ligase chain reaction in men and women following recommended therapy for uncomplicated 

gonorrhea. J Clin Microbiol 2002;40:3596–601.

7. Geisler WM. Duration of untreated, uncomplicated Chlamydia trachomatis genital infection and factors associated 

with chlamydia resolution: a review of human studies. J Infect Dis. 2010 Jun 15;201 Suppl 2:S104-13. 

Questions? Send e-mail to STD_Surv_Inquiry@cdc.gov